Starting phenix.real_space_refine on Wed Mar 12 14:43:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ukf_26579/03_2025/7ukf_26579.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ukf_26579/03_2025/7ukf_26579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ukf_26579/03_2025/7ukf_26579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ukf_26579/03_2025/7ukf_26579.map" model { file = "/net/cci-nas-00/data/ceres_data/7ukf_26579/03_2025/7ukf_26579.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ukf_26579/03_2025/7ukf_26579.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.068 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Hg 1 10.96 5 K 4 8.98 5 S 60 5.16 5 C 5252 2.51 5 N 1332 2.21 5 O 1356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8005 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2000 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' K': 4, ' HG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1842 SG CYS A 406 56.243 52.488 57.734 1.00 69.40 S Restraints were copied for chains: B, C, D Time building chain proxies: 4.66, per 1000 atoms: 0.58 Number of scatterers: 8005 At special positions: 0 Unit cell: (113.162, 112.336, 84.252, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Hg 1 79.96 K 4 19.00 S 60 16.00 O 1356 8.00 N 1332 7.00 C 5252 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 1.0 seconds 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1952 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 81.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 166 through 177 Processing helix chain 'A' and resid 181 through 206 Processing helix chain 'A' and resid 220 through 225 Processing helix chain 'A' and resid 225 through 250 Processing helix chain 'A' and resid 253 through 260 removed outlier: 3.602A pdb=" N SER A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 279 Proline residue: A 272 - end of helix Processing helix chain 'A' and resid 287 through 293 removed outlier: 4.020A pdb=" N VAL A 290 " --> pdb=" O GLY A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.972A pdb=" N PHE A 298 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG A 299 " --> pdb=" O PHE A 295 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS A 302 " --> pdb=" O PHE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 347 removed outlier: 5.088A pdb=" N SER A 322 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLU A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 368 removed outlier: 3.818A pdb=" N TRP A 362 " --> pdb=" O PRO A 358 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 400 Processing helix chain 'A' and resid 400 through 423 removed outlier: 4.252A pdb=" N VAL A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 177 Processing helix chain 'B' and resid 181 through 206 Processing helix chain 'B' and resid 220 through 225 Processing helix chain 'B' and resid 225 through 250 Processing helix chain 'B' and resid 253 through 260 removed outlier: 3.603A pdb=" N SER B 260 " --> pdb=" O ARG B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 279 Proline residue: B 272 - end of helix Processing helix chain 'B' and resid 287 through 293 removed outlier: 4.021A pdb=" N VAL B 290 " --> pdb=" O GLY B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.972A pdb=" N PHE B 298 " --> pdb=" O VAL B 294 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG B 299 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE B 300 " --> pdb=" O ARG B 296 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE B 301 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS B 302 " --> pdb=" O PHE B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 347 removed outlier: 5.087A pdb=" N SER B 322 " --> pdb=" O LYS B 318 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLU B 323 " --> pdb=" O SER B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 368 removed outlier: 3.818A pdb=" N TRP B 362 " --> pdb=" O PRO B 358 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR B 363 " --> pdb=" O ALA B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 400 Processing helix chain 'B' and resid 400 through 423 removed outlier: 4.252A pdb=" N VAL B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 177 Processing helix chain 'C' and resid 181 through 206 Processing helix chain 'C' and resid 220 through 225 Processing helix chain 'C' and resid 225 through 250 Processing helix chain 'C' and resid 253 through 260 removed outlier: 3.603A pdb=" N SER C 260 " --> pdb=" O ARG C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 279 Proline residue: C 272 - end of helix Processing helix chain 'C' and resid 287 through 293 removed outlier: 4.020A pdb=" N VAL C 290 " --> pdb=" O GLY C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.973A pdb=" N PHE C 298 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG C 299 " --> pdb=" O PHE C 295 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE C 300 " --> pdb=" O ARG C 296 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE C 301 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS C 302 " --> pdb=" O PHE C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 347 removed outlier: 5.087A pdb=" N SER C 322 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLU C 323 " --> pdb=" O SER C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 368 removed outlier: 3.818A pdb=" N TRP C 362 " --> pdb=" O PRO C 358 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR C 363 " --> pdb=" O ALA C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 400 Processing helix chain 'C' and resid 400 through 423 removed outlier: 4.252A pdb=" N VAL C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 177 Processing helix chain 'D' and resid 181 through 206 Processing helix chain 'D' and resid 220 through 225 Processing helix chain 'D' and resid 225 through 250 Processing helix chain 'D' and resid 253 through 260 removed outlier: 3.603A pdb=" N SER D 260 " --> pdb=" O ARG D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 279 Proline residue: D 272 - end of helix Processing helix chain 'D' and resid 287 through 293 removed outlier: 4.020A pdb=" N VAL D 290 " --> pdb=" O GLY D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 304 removed outlier: 3.972A pdb=" N PHE D 298 " --> pdb=" O VAL D 294 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG D 299 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE D 300 " --> pdb=" O ARG D 296 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE D 301 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS D 302 " --> pdb=" O PHE D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 347 removed outlier: 5.087A pdb=" N SER D 322 " --> pdb=" O LYS D 318 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLU D 323 " --> pdb=" O SER D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 368 removed outlier: 3.818A pdb=" N TRP D 362 " --> pdb=" O PRO D 358 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR D 363 " --> pdb=" O ALA D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 400 Processing helix chain 'D' and resid 400 through 423 removed outlier: 4.252A pdb=" N VAL D 404 " --> pdb=" O LEU D 400 " (cutoff:3.500A) 601 hydrogen bonds defined for protein. 1767 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.11 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2440 1.34 - 1.46: 1907 1.46 - 1.58: 3757 1.58 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 8196 Sorted by residual: bond pdb=" C VAL B 377 " pdb=" N PRO B 378 " ideal model delta sigma weight residual 1.333 1.320 0.013 1.17e-02 7.31e+03 1.22e+00 bond pdb=" C VAL A 377 " pdb=" N PRO A 378 " ideal model delta sigma weight residual 1.333 1.320 0.012 1.17e-02 7.31e+03 1.12e+00 bond pdb=" C VAL C 377 " pdb=" N PRO C 378 " ideal model delta sigma weight residual 1.333 1.320 0.012 1.17e-02 7.31e+03 1.11e+00 bond pdb=" C VAL D 377 " pdb=" N PRO D 378 " ideal model delta sigma weight residual 1.333 1.320 0.012 1.17e-02 7.31e+03 1.11e+00 bond pdb=" CB GLU A 346 " pdb=" CG GLU A 346 " ideal model delta sigma weight residual 1.520 1.494 0.026 3.00e-02 1.11e+03 7.38e-01 ... (remaining 8191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 10563 1.22 - 2.45: 451 2.45 - 3.67: 90 3.67 - 4.89: 20 4.89 - 6.12: 12 Bond angle restraints: 11136 Sorted by residual: angle pdb=" N LEU C 400 " pdb=" CA LEU C 400 " pdb=" C LEU C 400 " ideal model delta sigma weight residual 109.81 115.30 -5.49 2.21e+00 2.05e-01 6.17e+00 angle pdb=" N LEU D 400 " pdb=" CA LEU D 400 " pdb=" C LEU D 400 " ideal model delta sigma weight residual 109.81 115.27 -5.46 2.21e+00 2.05e-01 6.11e+00 angle pdb=" N LEU A 400 " pdb=" CA LEU A 400 " pdb=" C LEU A 400 " ideal model delta sigma weight residual 109.81 115.26 -5.45 2.21e+00 2.05e-01 6.07e+00 angle pdb=" N LEU B 400 " pdb=" CA LEU B 400 " pdb=" C LEU B 400 " ideal model delta sigma weight residual 109.81 115.24 -5.43 2.21e+00 2.05e-01 6.03e+00 angle pdb=" CA LEU C 271 " pdb=" C LEU C 271 " pdb=" N PRO C 272 " ideal model delta sigma weight residual 118.44 121.56 -3.12 1.59e+00 3.96e-01 3.85e+00 ... (remaining 11131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.14: 4010 10.14 - 20.28: 530 20.28 - 30.43: 176 30.43 - 40.57: 76 40.57 - 50.71: 12 Dihedral angle restraints: 4804 sinusoidal: 1772 harmonic: 3032 Sorted by residual: dihedral pdb=" CB MET D 333 " pdb=" CG MET D 333 " pdb=" SD MET D 333 " pdb=" CE MET D 333 " ideal model delta sinusoidal sigma weight residual 60.00 110.71 -50.71 3 1.50e+01 4.44e-03 8.93e+00 dihedral pdb=" CB MET A 333 " pdb=" CG MET A 333 " pdb=" SD MET A 333 " pdb=" CE MET A 333 " ideal model delta sinusoidal sigma weight residual 60.00 110.68 -50.68 3 1.50e+01 4.44e-03 8.93e+00 dihedral pdb=" CB MET B 333 " pdb=" CG MET B 333 " pdb=" SD MET B 333 " pdb=" CE MET B 333 " ideal model delta sinusoidal sigma weight residual 60.00 110.66 -50.66 3 1.50e+01 4.44e-03 8.93e+00 ... (remaining 4801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 629 0.026 - 0.051: 416 0.051 - 0.077: 183 0.077 - 0.102: 71 0.102 - 0.128: 17 Chirality restraints: 1316 Sorted by residual: chirality pdb=" CA VAL B 207 " pdb=" N VAL B 207 " pdb=" C VAL B 207 " pdb=" CB VAL B 207 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA VAL C 207 " pdb=" N VAL C 207 " pdb=" C VAL C 207 " pdb=" CB VAL C 207 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA VAL A 207 " pdb=" N VAL A 207 " pdb=" C VAL A 207 " pdb=" CB VAL A 207 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 1313 not shown) Planarity restraints: 1364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 357 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO C 358 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 358 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 358 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 357 " 0.030 5.00e-02 4.00e+02 4.48e-02 3.20e+00 pdb=" N PRO D 358 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO D 358 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 358 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 357 " 0.030 5.00e-02 4.00e+02 4.48e-02 3.20e+00 pdb=" N PRO B 358 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 358 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 358 " 0.025 5.00e-02 4.00e+02 ... (remaining 1361 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.86: 2973 2.86 - 3.43: 9594 3.43 - 4.00: 14762 4.00 - 4.57: 21588 4.57 - 5.14: 30209 Nonbonded interactions: 79126 Sorted by model distance: nonbonded pdb=" OG1 THR B 166 " pdb=" OE1 GLN B 169 " model vdw 2.290 3.040 nonbonded pdb=" OG1 THR D 166 " pdb=" OE1 GLN D 169 " model vdw 2.291 3.040 nonbonded pdb=" OG1 THR A 166 " pdb=" OE1 GLN A 169 " model vdw 2.292 3.040 nonbonded pdb=" OG1 THR C 166 " pdb=" OE1 GLN C 169 " model vdw 2.292 3.040 nonbonded pdb=" OH TYR D 188 " pdb=" O PHE D 303 " model vdw 2.339 3.040 ... (remaining 79121 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 166 through 424) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.360 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8196 Z= 0.261 Angle : 0.611 6.115 11136 Z= 0.349 Chirality : 0.041 0.128 1316 Planarity : 0.005 0.045 1364 Dihedral : 11.495 50.711 2852 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.27), residues: 1028 helix: 0.91 (0.18), residues: 796 sheet: None (None), residues: 0 loop : 0.83 (0.47), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 172 HIS 0.001 0.000 HIS C 414 PHE 0.010 0.001 PHE C 326 TYR 0.017 0.002 TYR C 188 ARG 0.002 0.000 ARG B 299 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.821 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.2284 time to fit residues: 37.6752 Evaluate side-chains 111 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.211537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.151833 restraints weight = 5692.573| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.68 r_work: 0.3286 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 8196 Z= 0.413 Angle : 0.626 6.446 11136 Z= 0.329 Chirality : 0.044 0.139 1316 Planarity : 0.005 0.047 1364 Dihedral : 3.982 13.602 1148 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.47 % Allowed : 6.25 % Favored : 93.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.26), residues: 1028 helix: 0.65 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.24 (0.46), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 172 HIS 0.003 0.001 HIS A 306 PHE 0.011 0.002 PHE D 326 TYR 0.021 0.002 TYR A 225 ARG 0.002 0.000 ARG B 305 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 104 time to evaluate : 0.891 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 105 average time/residue: 0.2076 time to fit residues: 30.0846 Evaluate side-chains 102 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain C residue 239 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 27 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 chunk 1 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 71 optimal weight: 0.1980 chunk 35 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.214901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.154217 restraints weight = 6132.971| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.89 r_work: 0.3322 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8196 Z= 0.189 Angle : 0.518 5.972 11136 Z= 0.270 Chirality : 0.038 0.133 1316 Planarity : 0.005 0.046 1364 Dihedral : 3.662 12.805 1148 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.12 % Allowed : 9.32 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.26), residues: 1028 helix: 1.04 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.06 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 172 HIS 0.001 0.000 HIS B 306 PHE 0.011 0.001 PHE D 326 TYR 0.018 0.001 TYR A 188 ARG 0.002 0.000 ARG B 305 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.894 Fit side-chains REVERT: A 257 PHE cc_start: 0.6627 (t80) cc_final: 0.6328 (t80) outliers start: 1 outliers final: 1 residues processed: 113 average time/residue: 0.1711 time to fit residues: 27.8223 Evaluate side-chains 104 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 98 optimal weight: 0.0970 chunk 80 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.214365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 110)---------------| | r_work = 0.3776 r_free = 0.3776 target = 0.153192 restraints weight = 6442.655| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.84 r_work: 0.3499 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8196 Z= 0.225 Angle : 0.526 5.846 11136 Z= 0.276 Chirality : 0.039 0.133 1316 Planarity : 0.005 0.045 1364 Dihedral : 3.597 12.609 1148 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.47 % Allowed : 11.56 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.26), residues: 1028 helix: 1.21 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.06 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 172 HIS 0.001 0.000 HIS C 306 PHE 0.011 0.001 PHE D 326 TYR 0.021 0.002 TYR B 273 ARG 0.001 0.000 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 118 time to evaluate : 0.792 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 119 average time/residue: 0.1552 time to fit residues: 27.1339 Evaluate side-chains 114 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 110 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain D residue 279 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 94 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.214959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.152551 restraints weight = 6664.915| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.04 r_work: 0.3320 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8196 Z= 0.208 Angle : 0.512 5.576 11136 Z= 0.268 Chirality : 0.039 0.133 1316 Planarity : 0.005 0.045 1364 Dihedral : 3.519 12.252 1148 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.94 % Allowed : 11.91 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.26), residues: 1028 helix: 1.35 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.00 (0.49), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 172 HIS 0.001 0.000 HIS B 306 PHE 0.011 0.001 PHE D 326 TYR 0.016 0.001 TYR A 188 ARG 0.001 0.000 ARG A 305 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.893 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 120 average time/residue: 0.1609 time to fit residues: 28.0914 Evaluate side-chains 118 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 113 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain D residue 227 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 3 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 chunk 94 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.215079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.164565 restraints weight = 6760.973| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.76 r_work: 0.3339 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8196 Z= 0.210 Angle : 0.517 5.388 11136 Z= 0.269 Chirality : 0.038 0.132 1316 Planarity : 0.004 0.044 1364 Dihedral : 3.480 12.156 1148 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.94 % Allowed : 12.50 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.26), residues: 1028 helix: 1.46 (0.18), residues: 840 sheet: None (None), residues: 0 loop : 0.08 (0.50), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 172 HIS 0.001 0.000 HIS B 306 PHE 0.012 0.001 PHE A 257 TYR 0.016 0.001 TYR A 188 ARG 0.001 0.000 ARG A 305 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.803 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 120 average time/residue: 0.1629 time to fit residues: 28.3500 Evaluate side-chains 123 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 279 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 65 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.214611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.167994 restraints weight = 6881.724| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.14 r_work: 0.3364 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8196 Z= 0.226 Angle : 0.521 5.184 11136 Z= 0.272 Chirality : 0.039 0.133 1316 Planarity : 0.004 0.044 1364 Dihedral : 3.484 12.183 1148 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.06 % Allowed : 13.33 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.26), residues: 1028 helix: 1.48 (0.18), residues: 840 sheet: None (None), residues: 0 loop : 0.08 (0.49), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 362 HIS 0.002 0.000 HIS B 306 PHE 0.011 0.001 PHE A 257 TYR 0.016 0.001 TYR A 188 ARG 0.003 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.769 Fit side-chains REVERT: C 411 ARG cc_start: 0.8409 (tmm-80) cc_final: 0.8151 (tmm-80) outliers start: 9 outliers final: 9 residues processed: 124 average time/residue: 0.1742 time to fit residues: 30.2800 Evaluate side-chains 126 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 279 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 57 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 54 optimal weight: 0.1980 chunk 82 optimal weight: 0.9980 chunk 84 optimal weight: 8.9990 chunk 67 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.215095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.164970 restraints weight = 6961.642| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 2.24 r_work: 0.3511 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8196 Z= 0.211 Angle : 0.512 5.162 11136 Z= 0.267 Chirality : 0.039 0.132 1316 Planarity : 0.004 0.044 1364 Dihedral : 3.454 12.121 1148 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.06 % Allowed : 13.33 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.26), residues: 1028 helix: 1.53 (0.18), residues: 840 sheet: None (None), residues: 0 loop : 0.07 (0.49), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 172 HIS 0.001 0.000 HIS D 306 PHE 0.015 0.001 PHE A 257 TYR 0.016 0.001 TYR A 188 ARG 0.001 0.000 ARG D 293 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.780 Fit side-chains REVERT: C 411 ARG cc_start: 0.8427 (tmm-80) cc_final: 0.8183 (tmm-80) outliers start: 9 outliers final: 9 residues processed: 128 average time/residue: 0.2113 time to fit residues: 39.0309 Evaluate side-chains 124 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 279 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 59 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.212730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.167626 restraints weight = 6875.868| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.16 r_work: 0.3492 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 8196 Z= 0.320 Angle : 0.569 5.530 11136 Z= 0.298 Chirality : 0.041 0.133 1316 Planarity : 0.005 0.044 1364 Dihedral : 3.588 12.253 1148 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.30 % Allowed : 13.56 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.26), residues: 1028 helix: 1.36 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.01 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 172 HIS 0.003 0.001 HIS B 306 PHE 0.018 0.002 PHE A 257 TYR 0.020 0.002 TYR B 273 ARG 0.003 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.788 Fit side-chains REVERT: C 411 ARG cc_start: 0.8501 (tmm-80) cc_final: 0.8260 (tmm-80) outliers start: 11 outliers final: 11 residues processed: 124 average time/residue: 0.1809 time to fit residues: 31.0278 Evaluate side-chains 126 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 279 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 15 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 37 optimal weight: 0.4980 chunk 29 optimal weight: 0.3980 chunk 11 optimal weight: 7.9990 chunk 98 optimal weight: 0.2980 chunk 44 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.215964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.152089 restraints weight = 6916.572| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.76 r_work: 0.3356 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8196 Z= 0.176 Angle : 0.509 5.172 11136 Z= 0.264 Chirality : 0.038 0.134 1316 Planarity : 0.004 0.044 1364 Dihedral : 3.443 12.352 1148 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.83 % Allowed : 14.15 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.26), residues: 1028 helix: 1.99 (0.18), residues: 796 sheet: None (None), residues: 0 loop : 0.38 (0.44), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 172 HIS 0.001 0.000 HIS A 306 PHE 0.009 0.001 PHE D 326 TYR 0.023 0.002 TYR B 273 ARG 0.002 0.000 ARG B 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 0.866 Fit side-chains REVERT: A 273 TYR cc_start: 0.7890 (t80) cc_final: 0.7675 (t80) REVERT: A 346 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7490 (tp30) REVERT: B 301 PHE cc_start: 0.7726 (m-80) cc_final: 0.7353 (m-10) REVERT: C 301 PHE cc_start: 0.7692 (m-80) cc_final: 0.7306 (m-10) REVERT: C 411 ARG cc_start: 0.8255 (tmm-80) cc_final: 0.8044 (tmm-80) REVERT: D 301 PHE cc_start: 0.7715 (m-80) cc_final: 0.7308 (m-10) outliers start: 7 outliers final: 6 residues processed: 133 average time/residue: 0.1874 time to fit residues: 35.0343 Evaluate side-chains 130 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 124 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 239 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 80 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 chunk 58 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.214685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.151391 restraints weight = 6838.318| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.98 r_work: 0.3335 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8196 Z= 0.219 Angle : 0.520 5.207 11136 Z= 0.271 Chirality : 0.039 0.132 1316 Planarity : 0.004 0.044 1364 Dihedral : 3.439 12.170 1148 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.94 % Allowed : 14.15 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.26), residues: 1028 helix: 1.94 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.36 (0.43), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 362 HIS 0.002 0.000 HIS B 306 PHE 0.017 0.001 PHE A 257 TYR 0.021 0.002 TYR D 273 ARG 0.002 0.000 ARG D 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5189.34 seconds wall clock time: 90 minutes 19.16 seconds (5419.16 seconds total)